Update README.md

README.md

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 # tiger
 Identifying rapidly-evolving characters in evolutionary data
 
-## About Tiger
+## Usage
+```
+****************
+TIGER Help:
+****************
 
-TIGER is open source software for identifying rapidly evolving sites (columns in an alignment, or characters in a morphological dataset). It can deal with many kinds of data (molecular, morphological etc.). Sites like these are important to identify as they are very often removed or reweighted in order to improve phylogenetic reconstruction. When a site is changing very quickly between taxa it might not hold much phylogenetic information and therefore might simply be a source of noise. Use of TIGER can (a) allow you to see the amount of rapid evolution and noise in your alignment and (b) provide a quick and easy way to remove as many of the “noisy” sites as possible.
+TIGER: Tree-Independent Generation of Evolutionary Rates
 
-TIGER uses conflict between site patterns as a proxy for rapid evolution; that is, a site that does not conflict with other sites in the alignment is generally a very slowly evolving or constant site. A site with lots of conflict is considered rapidly evolving (Cummins & McInerney, Systematic Biology, 2011). TIGER rates the conflict and categorizes the sites based on the rates. In this software the categories are called bins and are user definable (see manual for further details). Bin1 will contain the constant sites and the bin with the highest number will contain the most rapidly evolving sites.
+(Developed by Carla Cummins in the lab of James Mc Inerney, NUI Maynooth, Co. Kildare, Ireland)
+
+-Options:
+
+-in        Specify input file. File must be in FastA format and must be aligned prior.
+           Datasets with uneven sequence lengths will return an error.
+
+-v         Returns current TIGER version.
+
+-f         Changes output formatting options.
+           -f s: sorts sites depending on their agreement score
+           -f r: displays rank values rather than bin numbers
+           -f s,r: displays sorted ranks (*Be sure to put only a "," NO SPACE!)
+           
+           Default prints bin numbers unsorted.
+
+-b         Set the number of bins to be used.
+           -b <int>: Sites will be placed into <int> number of bins. <int> is a whole number.
+
+           Default is 10
+
+-rl       A list of the rate at each site may be optionally written to a specified
+          file. 
+          -rl <file.txt> : writes list of the rates at each site to file.txt.
+
+-ptp      Specifies that a PTP test should be run. *Note: this option has a huge 
+          effect on running time!
+
+-z        Number of randomisations to be used for the PTP test. 
+          -z <int>: each site will be randomised <int> times. <int> is a whole number.
+
+	 Default is 100
+
+-p       Specify p-value which denotes significance in PTP test.
+         -p <float>: site will be denoted as significant if p-value is better than <float>.
+                     <float> is a floating point number.
+
+         Default is 0.05
+
+-pl      Write a list of p-values to a specified file.
+         -pl <file.txt>: writes list of p-values for each site to file.txt.
+
+-u       Specify unknown characters in the alignment. Unknown characters are omitted from 
+         site patterns and so are not considered in the analysis.
+         -u ?,-,*: defines ?, - and * as unknown characters. (*Be sure to put only a comma
+                   between characters, NO SPACE!!)
+         
+         Default is ? only
+
+```
 
 ## System Requirements
 
-TIGER is implemented in Python, so it should run on most computer platforms.
+- Python 3.x.
 
-For UNIX machines, a working version of Python 3.x is required. On Windows machines, TIGER comes with everything it needs and requires no further installations.
+## Note
 
+Version 1.04 is made by Guoyi Zhang instead of other original authors. So, please cite this repository.
+
+## Citation
+
+- Cummins, C.A. and McInerney, J.O. (2011) A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases. Systematic Biology 60 (6) 833-844. doi: 10.1093/sysbio/syr064. 
+
+- Zhang G. (2022) TIGER version 1.04. https://github.com/starsareintherose/tiger